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Nucleic Acids Research 2006 34(Web Server issue):W733-W737; doi:10.1093/nar/gkl265
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article

GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface

Alexander Loß, Roland Stenutz1, Eberhard Schwarzer2 and Claus-W. von der Lieth*

German Cancer Research Centre, Central Spectroscopic Department –B090 Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany 1 Stockholm University, Department of Organic Chemistry SE-106 91 Stockholm, Sweden 2 University Hildesheim, Institute for Physics and Technical Informatics Marienburger Platz 22, D-31141 Hildesheim, Germany

*To whom correspondence should be addressed. Tel: +49 6221 424541; Fax: +49 6221 424554; Email: w.vonderlieth{at}dkfz.de

Received February 14, 2006. Revised March 2, 2006. Accepted March 31, 2006.

GlyNest and CASPER (www.casper.organ.su.se/casper/) are two independent services aiming to predict 1H- and 13C-NMR chemical shifts of glycans. GlyNest estimates chemical shifts of glycans based on a spherical environment encoding scheme for each atom. CASPER is an increment rule-based approach which uses chemical shifts of the free reducing monosaccharides which are altered according to attached residues of an oligo- or polysaccharide sequence. Both services, which are located on separate, distributed, servers are now available through a common interface of the GLYCOSCIENCES.de portal (www.glycosciences.de). The predictive ability of both techniques was evaluated for a test set of 155 13C and 181 1H spectra of assigned glycan structures. The standard deviations between experimental and estimated shifts (1H; 0.081/0.102; 13C 0.763/0.794; GlyNest/CASPER) are comparable for both methods and significantly better than procedures where stereochemistry is not encoded. The predictive ability of both approaches is in most cases sufficiently precise to be used for an automatic assignment of NMR-spectra. Since both procedures work efficiently and require computation times in the millisecond range on standard computers, they are well suited for the assignment of NMR spectra in high-throughput glycomics projects. The service is available at www.glycosciences.de/sweetdb/start.php?action=form_shift_estimation.


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